The word “throughput”, as opposed to output, refers to the efficiency of delivery rather than the actual delivery to be had in one burst.
In fighting games, there is a balance between speed and power that ultimately determines how efficient a character is at doing damage. This depends on a number of factors, including the damage done by a typical combo, and unlike the actual damage done itself, offensive throughput is difficult to quantify in exact terms because it is slightly subjective (and depends on every trick one knows about the character).
Regardless, it is still worth determining what one’s own throughput is with certain characters, and how to raise it. It’s all about obtaining victory faster.